title: Pinda: a web service for detection and analysis of intraspecies gene duplication events.
abstract: We present Pinda, a Web service for the detection and analysis of possible duplications of a given protein or DNA sequence within a source species. Pinda fully automates the whole gene duplication detection procedure, from performing the initial similarity searches, to generating the multiple sequence alignments and the corresponding phylogenetic trees, to bootstrapping the trees and producing a Z-score-based list of duplication candidates for the input sequence. Pinda has been cross-validated using an extensive set of known and bibliographically characterized duplication events. The service facilitates the automatic and dependable identification of gene duplication events, using some of the most successful bioinformatics software to perform an extensive analysis protocol. Pinda will prove of use for the analysis of newly discovered genes and proteins, thus also assisting the study of recently sequenced genomes. The service's location is http://orion.mbg.duth.gr/Pinda. The source code is freely available via https://github.com/dgkontopoulos/Pinda/.
authors.affiliation: Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, 68100 Alexandroupolis, Greece.
authors.forename: Dimitrios-Georgios
authors.initials: DG
authors.lastname: Kontopoulos
authors.forename: Nicholas M
authors.initials: NM
authors.lastname: Glykos
mesh_terms: D020440:Gene Duplication; D020407:Internet; D017422:Sequence Analysis, DNA; D012984:Software; D014584:User-Computer Interface
keywords: Gene duplication; Phylogenetic analysis; Sequence analysis; Web service